Chase Clark

It would sometimes be nice to be able to take the information in the metadata table (e.g. genus) and append it to the name of the sample (eg in the...

It would be helpful to include instructions on how to submit the error log for issues like: #38

MALDI and MSQL

5

It's turning out to be quite difficult to get MALDI data into a format that works with MSQL. Note: I don't currently have access to any Vendor software to see...

:memo: Update Contributor Covenant

2

Replace nf-core code of conduct template with Contributor Covenant template https://www.contributor-covenant.org/version/2/1/code_of_conduct/code_of_conduct.md

Docs: Fix conda command ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code...

Missing example data causes gdown script to fail

4

There are some files that don't exist for all of the example datasets which causes the script to fail: ``` Access denied with the following error: Cannot retrieve the public...

Change arg name `--norm-output` for `autometa-kmers` entrypoint

2

Don't change this yet, but the following argument name is confusing. It's an input path to a tsv of normalized kmer counts but is named `norm-output`. https://github.com/KwanLab/Autometa/blob/baf61c04dddf5b33bb825dba2841de1e38dffefe/autometa/common/kmers.py#L736-L740 The command's output...

Look into using taxon result limited blastp instead of top-n limited

1

Taxon assignment is currently performed by running DIAMOND blastp on contig proteins, finding the LCA and majority vote. Currently, the blast result simply returns the top 200 database hits which...

Fix BLAST results protein to taxonomic accession assignment

1

Currently the documentation instructs and the code downloads `prot.accession2taxid.gz` which doesn't have all of the `nr` accessions. Proteins that aren't found in `prot.accession2taxid.gz` are assigned to root which results in...